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Hierarchical population genetic structure and signatures of adaptation in Lates calcarifer

Matthew Campbell , Joy Becker

Abstract

Context Lates calcarifer known as barramundi perch, is widespread in the tropical Indo-Pacific region and is an important taxon in aquaculture, recreational and commercial fisheries. With mitochondrial barcoding study of barramundi perch, three clear mitochondrial clusters have emerged. Aims To test for congruent signal between mitochondrial and nuclear genomes and to test for population genetic structure. We further estimated the evolutionary significance of genetic clusters in terms of signatures of adaptation in the nuclear genome. Methods We conducted analyses of mitochondrial sequence data and whole-genome sequencing data from across the range of barramundi perch (n=60). We applied phylogenetic, phylogenomic and population genetic methods. Key Results We find congruent signal for three lineages of barramundi perch in both the mitochondrial and nuclear genomes. Substantial genetic differentiation is present between and within all three lineages of barramundi perch. Calculation of divergence times indicates a separation of ~ 7.38 million years ago, and another separation dating to ~1.16 million years ago. Conclusions Three lineages of barramundi perch are apparent, with candidate adaptive loci identified between and within each lineage, indicating both discreteness and evolutionary significance. Implications This study highlights the need for comprehensive sampling and integrative study of genotypes and phenotypes across the range of barramundi perch.

MF24227  Accepted 05 November 2024

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